By Vivien Marx
This article was posted on Feb. 24.
Sage Bionetworks said this week that it has received a $6.7 million grant from the National Cancer Institute making it a Center for Cancer Systems Biology under NCI's Integrative Cancer Biology Program, which is dedicated to developing and implementing computational models of cancer-related processes.
The Sage grant is the first CCSB award that has been disclosed. According to a request for applications for the program issued last year, NCI plans to commit a total of approximately $22.5 million per year to fund up to nine centers for up to five years.
The CCSBs expand on the initial ICBP program that NCI kicked off in 2003 by emphasizing computational approaches to cancer research. The centers are to address an "overarching cancer biology problem" involving, for example, gene expression, metabolic or signaling networks, or temporal processes such as cancer progression, with a three-pronged effort that includes experimental systems biology, mathematical modeling or computer simulation, and educational efforts.
Sage joins existing ICBP centers at Case Western University, the Dana-Farber Cancer Institute, Duke University, Lawrence Berkeley National Laboratory, Massachusetts General Hospital, MIT, Ohio State, Stanford, and Vanderbilt universities.
The centers are expected to develop "testable models" that will act as a framework for ongoing experimentation, data analysis, and validation. According to the RFA, a given computational model "should allow one to predict the biological state under investigation and to predict how the natural process will behave in various circumstances." New experimental data will help to refine model development, according to the RFA.
Sage Bionetworks president Stephen Friend said in a statement that the NCI grant is an "endorsement for our young organization and validates our vision to establish a contractor-based integrative genomics and network biology resource to accelerate drug development."
The money, which will support the center's operation and the training of four postdoctoral researchers each year, forms "the base for the first four years of the program," Friend told BioInform via e-mail this week.
Sage Bionetworks' training and research program, as well as the forthcoming Sage Commons platform, will "bring a new dimension" to the ICBP centers program, Dan Gallahan, who directs the NCI program, said in a statement.
At first glance Sage, which Friend described as an "academic-corporate startup hybrid," may not be an obvious fit in the circle of large academic groups that currently comprise the ICBP centers, but Friend said the organization has "a small but outstanding group of researchers" with a track record of academic and commercial success.
"It is a bit different for such a small group to run with the big dogs, but Sage is all about doing genomic science differently and it is a real credit to NIH that they have been willing to think outside the box with us," Friend said.
He explained that the funds will support two pairs of trainees, "one new and one senior pair," each year as well as mentor time, high-performance computing costs, and travel for the trainees to do "externships" at other centers.
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Education is not a departure for the non-profit but rather part of its core themes, he explained, which also include research and platform building, creating what Sage calls "the Commons." The NCI's ICBP program encouraged Sage to develop its CCSB proposal, he said.
One reason behind the education pillar of the organization is that "advanced integrative genomics skills are rare," he explained. Sage must also play a training role in order to "catalyze the formation of a participant community for the Sage Commons," Friend said. "We do not want to be primarily in the business of consulting."
Do the Cross-Over
The first step in establishing the center is to recruit "cross-over post-docs," who are to be "imaginative, energetic math and biology experts to form the initial trainee team," Friend said. They will join the center for two years. Additional trained scientists, "seasoned model builders and systems biologists," will be added to the mix to mentor the students in their research projects, Friend said.
He said he hopes that "this novel strategy" of pairing physicists and biologists/clinicians "will allow us to train a small portion of the needed systems biologists and network biologists required in this nascent field."
Sage Bionetworks and its partners also plan to hold "periodic workshops to train, and to learn from, the broader genomics community as well," Friend said.
Trainees might arrive with experimental or in silico datasets in hand but that is not a prerequisite, he said. The goal of the venture is "to develop professionals who can work with and lead dynamic teams to build, analyze, and use predictive disease models to advance therapeutic and diagnostic innovation," he said. "Many of our newly enabled collaborators will be contributing their data that the students will be able to dig into."
The center will be based at the non-profit's facilities at the Fred Hutchinson Cancer Research Center in Seattle, and trainees will benefit from colleagues there and at the University of Washington, he said.
Teaching will be handled by Sage's "senior staff" as well as visiting scientists from around the world who will combine didactic approaches with mentoring, he said.
The Sage program will also support research collaborations with Johns Hopkins University, the University of Hong Kong, DFCI, the Netherlands Cancer Institute, the Fred Hutchinson Cancer Research Center, and others to generate new datasets, he said.
The research projects will begin with a focus on breast, colon, liver, and pancreatic cancer, and the computational models developed will be validated experimentally to test their accuracy and refine their models, Sage said.
The plan is to work with other centers "to test their data sets with our tools and vice versa as a direct test of the robustness and value of the disease models," Friend said. "This will be an important step in validating integrative genomics and building a participant community."
An additional benefit for Sage, Friend said, is that this project help the firm align itself with ongoing NCI efforts such as the Cancer Genome Atlas and the Cancer Biomedical Informatics Grid.
The new grant adds to the funding Sage has been collecting from several partnerships and foundations. Last Spring, Merck researchers Friend and Eric Schadt formed Sage with an undisclosed amount of data and logistical support from Merck. In January, Sage signed a partnership with Pfizer for an undisclosed amount of research funding [BioInform 1-15-2010].
Last October biopharmaceutical services firm Quintiles made a donation of an undisclosed sum. Other support comes from the CHDI Foundation, which aims to help develop drugs for Huntington's disease; the Canary Fund, which is focused on cancer detection; and Science Commons.